<div dir="ltr">i actually mean the log-likelihood, which is the target function typically optimized in phenix.refine. If you compute the log likehood for the test/free set instead, one might overcome bias issues, if any are present.<div><br></div><div>P</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 11 February 2015 at 21:56, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Peter,<br>
<br>
you suggest to calculate "the (free) likelihood".. May I ask:
specifically likelihood of what you are suggesting to calculate and
what is "free" in this context? I guess I'm just lost in jargon,
sorry!<br>
<br>
Thanks,<br>
Pavel<div><div class="h5"><br>
<br>
<br>
<div>On 2/11/15 8:08 PM, Peter Zwart wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Dear All,</div>
<div><br>
</div>
How meaningful are the second derivative based estimates
obtained via full matrix inversion when the gradient is not 0
(i.e. when not in the minimum)? I can understand that when you
are working with high-resolution data and your R-value is close
to 0, things could work, but what happens when around a more
challenging 2A?
<div><br>
<div>If you are interested in the uncertainty of the
occupancy, I recommend not doing any refinement, but just
generate a list of occupancies and B-values for the atom of
interest and compute the (free) likelihood for each model.
Subsequent normalisation of the neg-exponent of these
values, should provide you with an answer that could be just
as believable as any other method around. A little bit of
python scripting should do the trick quite easily.</div>
<div><br>
</div>
<div>Both the full matrix inversion and the suggestion above
probe the steepness of the data-agreement hole the structure
is sitting in. Pavels suggestion explores the spread of
local minima around the starting configuration. I am not
sure what method is more appropriate, perhaps it is
instructive to know what problem you are trying to solve.</div>
<div><br>
</div>
<div>HTH</div>
<div>P</div>
<div> </div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 11 February 2015 at 16:13, Masaki
UNNO <span dir="ltr"><<a href="mailto:unno19@mx.ibaraki.ac.jp" target="_blank">unno19@mx.ibaraki.ac.jp</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all<br>
<br>
Thank you very much for your suggestions.<br>
I will try making a number of models in which the atom has
different<br>
occupancies (e.g. 0.1-1.0). Then, I will refine them by
restraining the<br>
B-factors.<br>
Actually, our structure contains some reaction intermediates
not only the<br>
substrate. So I would like to estimate the ratio.<br>
<br>
Best regards<br>
<span><font color="#888888"><br>
Masaki<br>
</font></span><span>-----Original
Message-----<br>
From: <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a><br>
[mailto:<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>]
On Behalf Of Pavel Afonine<br>
</span><span>Sent: Thursday, February 12,
2015 6:36 AM<br>
To: Dale Tronrud; <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
Subject: Re: [phenixbb] How should we estimate the
"uncertainty" of the<br>
occupancy of an atom?<br>
<br>
</span>
<div>
<div>Hi Dale,<br>
<br>
> P.S. I'll look up the paper you reference but my
university does not<br>
> subscribe to acta Cryst and getting those papers
takes time.<br>
<br>
it is open access:<br>
<br>
<a href="http://phenix-online.org/papers/wd5073_reprint.pdf" target="_blank">http://phenix-online.org/papers/wd5073_reprint.pdf</a><br>
<br>
All the best,<br>
Pavel<br>
<br>
<br>
<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div>-----------------------------------------------------------------<br>P.H. Zwart<br>Staff Scientist<br>Berkeley Center for Structural Biology, Science lead<br>Lawrence Berkeley National Laboratories<br>1 Cyclotron Road, Berkeley, CA-94703, USA<br>Cell: 510 289 9246<br>SASTBX: <a href="http://sastbx.als.lbl.gov" target="_blank">http://sastbx.als.lbl.gov</a></div><div>BCSB: <a href="http://bcsb.als.lbl.gov" target="_blank">http://bcsb.als.lbl.gov</a><br></div><div>PHENIX: <a href="http://www.phenix-online.org" target="_blank">http://www.phenix-online.org</a></div><div>-----------------------------------------------------------------</div></div></div>
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